Most global hotspots of biodiversity and endemism are in montane regions. One explanation is that montane regions have intrinsically higher speciation rates than lowland regions because complex mountain topography and climate variation facilitate genetic isolation among populations. Here, we ask from an intraspecific perspective whether frog species whose haplotypes are connected by topographically/climatically complex regions display strong genetic isolation (greater scaled genetic distances), compared with species whose haplotypes are connected by less complex regions. We analysed published DNA sequences of several frog species from tropical Central and South America for the mitochondrial cob, cox1 and 16S rRNA genes. Pairwise genetic distances among haplotypes within each species were scaled to the geographic distances between each pair of haplotypes. Topographic complexity was positively correlated with scaled genetic distances, and isolation-by-resistance was supported only in species from more topographically complex regions. This suggests that heterogeneous topographies increase landscape resistance, which in turn favours the appearance of isolation-by-resistance. Moreover, we found that the potential barriers that restrict gene flow within species are more closely related to factors associated with temperature and topography than to precipitation.